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Old 07-03-2017, 10:48 AM   #1
skm
Junior Member
 
Location: india

Join Date: Nov 2011
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Smile [ddRAD] on removal of duplicate reads

Hi All,

Is it advisable to remove duplicate reads from double digest RAD (ddRAD) data generated on Illumina Hiseq platform ?

Regards,
Krishna
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Old 07-03-2017, 06:40 PM   #2
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

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Default

ddRAD libraries has two types of duplicates:

1- PCR duplicates
2- duplicates rising from input genome equivalent used for dig-lig

As most of ddRAD protocols does not use UMIs, it is not possible to distinguish those.

Throughout analysis a minimum coverage is used to form stacks of RAD-tags, catalog and estimate zygosity for the called genotypes so duplicates should not be removed.
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